Hi Tonja and welcome to Binkybunny
Is there a reason why there are two litter boxes in her cage? One should be sufficient as normally people only use two or more litter boxes if the bunny is free roam – one for the cage and one outside somewhere in the room where the bun roams. It’s also easier for the rabbit to learn if there is only one box.
What litter are you using? I would recommend wood pellets instead of paper bedding as the pellets can absorb more pee and smell. That being said, changing the litter every 2 days is actually quite normal. Most people change it every 2-3 days. Personally I change it daily if possible.
2 months old is indeed too young to be spayed. Unfortunately until she is spayed, it’ll be very difficult to litter train her fully as she will always have the hormonal instinct to mark her territory.
Every rabbit will usually have a favourite corner they love to pee in. This may not be the corner you originally put the litter box in, so if you manage to find Peps’ favourite corner, put her litter box there instead along with the hay rack – that may help.